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In ancient times, a monstrous sunspot called the Tartarus sunspot (which occurs every 4,000-4,500 years) was prevented from causing major flooding and catastrophic weather by the use of the Golden Capstone. This Capstone was later divided up by Alexander the Great into its component parts, with one piece hidden within each of the seven wonders of the world. If and when they are reunited and replaced on the top of the Great Pyramid during another sunspot event, they can bring 1,000 years of peace or power for the nation which possesses them.

In 1996, Jack West Jr and Max Epper (also known as Wizard) are in a Ugandan volcano attempting to prevent Francisco del Piero, a Vatican priest leading a European coalition representing the Catholic Church, from stealing the newborn son of the Oracle of Siwa, able to read the mysterious language known as the Word of Thoth. However they are too late, and while checking the mother's body, Jack discovers she has another child, a daughter, and he and Epper retrieve her, but are hindered by the lava blocking their exit. Jack loses his left arm disabling the trap, and they head off to a meeting between seven "small' nations (Canada, Australia, Ireland, the United Arab Emirates, Spain, Jamaica and New Zealand) concerning the upcoming Tartarus event.

Once Epper gives his brief, it is agreed that one person from each country (save for Ireland, who provide two) will hide the girl at a farm in Kenya, named Lily, and raise her until she can begin translating the clues in the Callimachus text leading to each of the Wonders' location, wherein lies a piece of the Capstone. Over the years, Lily grows up to be very inquisitive and intelligent thanks to the teachings of the team and Epper's wife, Doris, while Epper builds a mechanical prosthetic arm for Jack. The coalition of Minnows are joined seven years into the mission by Benjamin Cohen (Stretch) of the Israeli Mossad, who threaten to expose their plans if they cannot join, to the chagrin of Aziz al Anzar al Abbas (Pooh Bear).

In 2006, seven days before this sunspot is due, the ten-year-told Lily becomes able to dechiper the first verse of the ancient text, and so the team heads to an ancient mine in the Sudan to locate the head of the Colossus of Rhodes Piece. Though they are able to best the European coalition and retrieve the Pieve first, an American force known as CIEF (the Commander-in-Chief's In Extremis Force, which covertly represents the Freemasons) captures the team after killing Enrique Velacruz (Noddy). The CIEF team leader, Cal Kallis, takes their Piece and is ordered to kill everyone except for Jack and Lily, but luckily they manage to escape in Jack's plane, the Halicarnassus, piloted Sky Monster.

With Lily's help, Jack and Epper determine the next Piece is at Hamilcar's Refuge on the coast of Tunisia, and because they hold the only clue between the Callimachus text and a seperate scroll, believe that the Americans and Europeans cannot locate it. Upon entering the refuge, they discover the remains of a Nazi U-boat which had belonged to two Nazi archaeologists, Hans Koenig and Herman Hessler, during their search for the Capstone. However CIEF has somehow also located the refuge, and as they race to the Piece, Jack learns that Colonel Marshall Judah, a former mentor of his during his time training at Coronado, is leading the CIEF team. After making their way through the trap system, they learn that in addition to the Mausoleum of Halicarnassus Piece, there is also the mirror from the Lighthouse of Alexandria and its matching Piece. However, they are outmatched by the CIEF and are forced to leave the Pieces (though Jack manages to take photos of the inscriptions on each Piece) and escape.

As Jack confides in Epper his suspicion that someone on their team is telling the Americans of their locations, Epper reveals that the next two clues don't give any real indication of the Wonders' locations. Needing help, the team springs Mustapha Zaeed, the world's foremost authority on the Capstone and the Seven Wonders and a known terrorist, from Guantanamo Bay. With Zaeed's help they learn that the Statue of Zeus at Olympia Piece is in the Louvre in Paris, and the Temple of Artemis Piece is in St. Peter's Basilica. Jack, Lilly, Pooh, Stretch and Liam Kissane (Big Ears) retrieve the Zeus Piece, while also learning how to locate Alexander the Great's tomb, where the final Piece lies. Epper, Zoe Kissane and V.J. Weatherly (Fuzzy) are unable to take the Artemis Piece due the presence of guards in the Basilica, and so instead have Epper memorise the inscription on it, however they are captured by del Piero's men once they report back to Jack's team.

Unaware of their teammates' capture, Jack's team returns to their Kenyan farm, only to be ambushed by Judah and the CIEF. Doris is killed for giving Lily a secret warning, and Big Ears sacrifices himself to get Lily back onto the Halicarnassus. Unfortunately, Big Ears is carrying their Piece, which Judah seizes as the coalition team escapes. Judah contacts them soon afterwards, taunts them they cannot beat him and taking delight in informing them of the capture of Epper's team. With no other options other than to attempt to get the next Piece first, Jack decides that they must locate the Hanging Gardens of Babylon.

Both Jack and Zaeed manage to deduce the Gardens' location in Iraq, but upon arriving at the entrance the team is apprehended by an Israeli strike team, as Stretch (unknowingly) led them to the location. West is forced to lead Avenger and his people to the Piece, and at one stage, while caught in a defending trap, Jack becomes encouraged to find the escape solution when Lily calls him "daddy". Once they find the Piece, Jack and Pooh are left for dead while Zaeed escapes from the Israelis. With the Americans arriving, Stretch is ordered by Avenger to leave Lily in a quick sand trap, but he cannot bring himself to do it and so abandons his countrymen to rescue her. Ultimately, this decision saves his life when he and Lily are captured by Judah, while the other Israelis are executed and their Piece taken.

Jack and Pooh narrowly escape as Judah has the gigantic stalactite comprising the Gardens brought down on top of them, only to end up caught in a trap. Zaeed, who has already bypassed it, abandons them and reveals that Lily will die for the Capstone incantation to work. After getting through the trap thanks to Jack's falcon Horus, the pair regroup with Sky Monster on the Halicarnassus. There, Jack realises that he has been the one the Americans have been tracking, as he has had a tracking chip in his head since training with Judah at Coronado years earlier. After disabling it, he, Pooh and Sky Monster head off to Egypt with the intention of preventing the CIEF from performing the ceremony of power.

Meanwhile, del Piero speaks with Epper's captured team, and reveals Alexander, the son of the Oracle whom he kidnapped years earlier and has raised since. Despite his plan to kill the Americans and take their Pieces when they arrive at Cairo, del Piero's men are all killed, while he, Alexander and Epper's team are captured along with the Artemis Piece, leaving the Americans to only need to retrieve the Piece from the tomb of Alexander the Great

On the day of the Tartarus rotation, Judah reveals that the Americans have been working with Hans Koenig, the Nazi archaeologist who has survived into the present day, and he helps them to locate the final Piece of the Capstone from Alexander's tomb in Luxor. Judah brings all of his prisoners together, and thus Lily meets her twin for the first time, however she dislikes Alexander for the attitude that del Piero has brainwashed him with over the years. Judah takes the whole Capstone, Epper, Lily, del Piero and Alexander to the Giza Pyramid, and has Alexander placed in the chamber beneath it, along with one deben of American soil, to ensure the ritual of power works.

However, Jack and his team arrive to stop them, surprising their enemy with the hovering function Epper had built into the Halicarnassus while also providing Pooh Bear and Sky Monster with a battle platform. Judah tries to carry out the ritual, but Alexander crawls out to save himself from death, unwittingly ensuring its failure. The rest of Jack's captured team escapes and join in fighting the CIEF forces, and del Piero, Koenig and Kallis each perish during the battle. In the chaos, however, Zaeed (having stowed away on the Halicarnassus after escaping the Hanging Gardens) carries out the ritual successfully after Lily crawls into the recess chamber willingly for him.

Jack, however, had previously switched the soil of Zaeed's homeland with his own, and so now Australia has 1000 years of power. After killing Zaeed and Judah (throwing the latter in the engines of the Halicarnassus), the victorious team of minnows departs Giza, taking with them the entire Capstone. Stretch is forgiven by the others and now fully accepted as one of them, and Lily reveals that she survived by (unlike Alexander) going into the chamber willingly, as a scroll she read earlier explained. Lily then expresses her sympathy to Zoe and Epper for the loss of their loved ones.

Three weeks later, after another meeting of the small nations has concluded and agreed not to reveal Australia's invulnerability, Epper and Zoe accompany Lily across Central Australia, reuniting with Jack at his new farm. There, he reveals he has collected some of the Ancient Wonders they encountered during their mission, as well as the Capstone, and presents Zoe with a White Desert rose he recovered from the Hanging Gardens.

A World War II U-boat is found in Hamilcar's Refuge, used by a Nazi expedition to find the piece. This references various popular culture items such as Indiana Jones and the Raiders of the Lost Ark and The Last Crusade showing Nazi Germany as setting out to recover occult archaeological artefacts.

Hans Koeing, leader of the Nazi expedition, now working for the CIEF team, references various other Nazis pardoned and employed by the United States, such as Wernher von Braun.

The Callimachus Text is a vital plot device, referring to Callimachus, the real-life librarian of the Musaeum in Alexandria, who wrote the famous list of the seven wonders. Here he is held to have been privy to Alexander's splitting up the pieces and thus to have left coded references to that in his list.

There are numerous references made to Egyptian and Mesopotamian landmarks, notably tombs, monuments and obelisks.

West finds an extinct plant in the Hanging Gardens, and takes one to Australia. The power of Tartarus allows the plant to grow in Australia, and he gives one to Zoe.